If no windows are opened, it does not happen, but the phenomenon is pretty random, I can run 8 cores simulation on my i7 without a problem while sometime, just opening a 500 lines file with vi will make the Xorg goes 100% and I will get super slow dispay (< 1fps). If I close the terminal and restart I don't have this problem anymore.

Sometimes, closing a terminal with nothing running inside make Xorg go back to ~0% CPU.

I do not experience the problem with software rendered cinnamonI do not experience the problem with basic gnome

I paid attention to disable all the fancy panel applets.

I tried to get ride of java7 to see if that was the problem, without success.

(gnome-settings-daemon:3530): updates-plugin-WARNING **: failed to get upgrades: GDBus.Error:org.gtk.GDBus.UnmappedGError.Quark._pk_5ftransaction_5ferror.Code4: GetDistroUpgrades not supported by backendWindow manager warning: Buggy client sent a _NET_ACTIVE_WINDOW message with a timestamp of 0 for 0x2400041 (Workspace )Window manager warning: meta_window_activate called by a pager with a 0 timestamp; the pager needs to be fixed.Window manager warning: Buggy client sent a _NET_ACTIVE_WINDOW message with a timestamp of 0 for 0x2400003 (Eclipse )Window manager warning: meta_window_activate called by a pager with a 0 timestamp; the pager needs to be fixed.Window manager warning: meta_window_activate called by a pager with a 0 timestamp; the pager needs to be fixed.Window manager warning: Buggy client sent a _NET_ACTIVE_WINDOW message with a timestamp of 0 for 0x2404835 (Build Proj)Window manager warning: meta_window_activate called by a pager with a 0 timestamp; the pager needs to be fixed.Window manager warning: Buggy client sent a _NET_ACTIVE_WINDOW message with a timestamp of 0 for 0x2400114 (C/C++ - st) Window manager warning: meta_window_activate called by a pager with a 0 timestamp; the pager needs to be fixed.Window manager warning: meta_window_activate called by a pager with a 0 timestamp; the pager needs to be fixed.Window manager warning: Invalid WM_TRANSIENT_FOR window 0x2a00005 specified for 0x2a00003 (paraview).Window manager warning: meta_window_activate called by a pager with a 0 timestamp; the pager needs to be fixed.